The Return of Evangelion
by FerbFlecher151
Summary: A retelling of Neon Genesis Evangelion. Will start similar, but will change later on. Currently on Season 1. Shinji is a brand new pilot at NERV, but unknown to him, there are more enemies then just Angels...
1. S1,E1: Welcome to Nerv

This is a story I've been wanting to do for a while now, and it's based off my all time favourite anime Neon Genesis Evangelion.

Now the way this story is going to work is that it will be a episodic story with "seasons". The first season will be a retelling of the original series (with some pretty major differences to come later on), while later seasons will be my own original creations.

Now enjoy!

* * *

**Episode 1: Welcome to NERV**

Having tanks around everyday was rather intimidating. Well, according to Shinji at least.

It had been 11 years since his mother had died in a tragic accident. It was also during this time that his father had left him and sent him to live with his teacher. Shinji was always told that his father had "important things to do" and that he was going to change the world, but Shinji never truly cared about all of that. All he wanted was a father stayed for him, unlike the one he did have.

But last night, something strange happened. For once, his father actually called him.

He was having dinner when the phone ringed. His teacher was usually the one who picked it up first (Shinji always insisted that he did), but he was out during the time, so Shinji picked it up this time. He was shocked to hear his father on the other end, telling that he needed him, now more then ever. Shinji, usually doing what he was told, accepted the rather cryptic offer made by his father and left the next day without a word.

He waited outside for hours for his carpool to come and get him. He had no idea what the car was going to look like, or the person driving. Would it be his father? A co-worker? Friend? It was at this point he decided to call his father again to get more information. He had left his number before he hanged up.

"We're sorry," the automated machine on the other end said, "But due to the state of emergency, your call cannot be completed. We thank you for you cooperation." Shinji slammed the phone in frustration. How was he supposed to know what car was his?

Thinking about it, there hadn't been many cars around today. And what was the state of emergency the phone chick was talking about?

He looked both ways in search for at least one car. When he turned his head to the left however, he saw a blue haired girl in the distance, surrounded in fog. Shinji jumped in shock. Why was a girl, around his age, just standing there?

Maybe it was just a mirage. He looked away and then looked back again. The girl was gone. Shinji sighed. It was just a mirage.

Suddenly, just then, the ground violently shaked. The garage next to him rattled and the wires overhead shook. Shinji had to plug his ears due to the noise. He ground shook again. This time, it almost knocked Shinji off his feet. The shaking became closer, stronger and more frequent. Shinji turned to look, and he saw a giant creature. It was green in colour, with gill like things on it's shoulder's. It had a

rib cage in it's centre, with a skull like face. The military was following it.

"What is that thing?" Shinji murmured to himself as a he saw the creature move along it's merry way.

* * *

"Target is approaching rapidly," said a technician at NERV Headquaters.

"Pattern analysis confirmed blue. It's an angel!" yelled another one.

At the headquaters, 3 military personal sat down in front of a giant screen. All of them were gruff, older men, wearing the standard military uniform. Sitting behind them, however, was someone of greater note. This man wore red tinted glasses, and held his hand together with his elbows on the desk. Behind him stood an older man with grey hair.

"So, the angels have returned," the older man said.

"Indeed they have, Futyusuki," the man with the glasses said. This man's name was Gendo Ikari.

"All air forces," one of the military men said, "Fire at will!"

The aircraft started firing at the angel. The missile just kept bouncing off of it, or exploding without even the target.

The angel lifted it's right arm, and a long, purple spear came protruding outward. It glowed, and looked other worldly. It hit one of aircraft, piercing one of it's engine. It spun out of control, with the pilot screaming inside. It crashed onto the road, sending debris up in the air and cracking the road.

Unfortunately for Shinji, he was right next to the crash site. He was terrified out of his wits, and was knocked down by the force of the crash. The angel walked over to him, and stepped on the downed aircraft. He didn't know what to do. He was scared.

Then, from the left, a blue car came out of nowhere and opened it's doors. Inside there was a women with dark blue hair and sunglasses. She was strangely smiling.

"Sorry I'm late Shinji," she said, "Get in!" Shinji got up and went in as quickly as possible. The women closed the door and started driving away from the angel.

"What the hell was that thing?!" yelled Shinji. This was just one of his many questions.

"That was an angel. It's come to kill us all."

"...Well that's very assuring," Shinji said sarcastically.

* * *

"All missile hit the targets sir!" a technician said the men in the military. "Unfortunately, they were unable to cause any significant damage!"

"Damn it!" said one of the generals as he slammed his fist onto the table, shaking the ash tray next to him. "Why can't anything destroy this thing?" One of the other generals picked up a red phone.

"Looks like an AT Field," Futyusuki stated.

"Yes. It seems that conventional weapons have no effect at all," Gendo replied.

"Something has got to work!" another one of the general exclaimed, unsure of what to do. The 3rd general put down the red phone.

"High command has just order us to activate the contingency plan," he explained.

"You heard the man! Launch the N2 bomb!" The general yelled as NERV scrambled to get the plan underway.

* * *

"What are they doing?" said the blue haired women. She was looking outside her window, at the angel. Shinji was under her shoulder, looking as well. He had a lot questions, but obviously they weren't going to answered right now. Then the woman made a gasping noise. Shinji saw an object falling from the sky. He hoped that it wasn't what he thought it was...

"They're going to use an N2 bomb!" she yelled, "Get down!" She grabbed Shinji and pulled him down as quickly as possible. Shinji felt like he was being crushed.

He heard a deafing explosion far off in the distance. Despite it being a ways off, it still made his ears pop and ring. The shockwave reached them, and flipped the car over several times, wrecking it. Both Shinji and the women screamed at the top of their lungs. After a while, the shockwave subsided and both able to get out unscathed.

"Well, that went well," the woman said with cheery voice, "We're going to have turn this car over. You push there while I push over here." Shinji did as he told and stood with his back towards the car. The women did the same.

"Ok... on the count of three! 1.. 2.. 3!" The women grunted as pushed the car with all her might. Shinji did the same, but with much less enthusiasm. After a about 30 seconds the car flipped over. The women clapped her hands to get rid of the dirt on them.

"So, you must be Shinji Ikari, right?"

"Yeah," answered Shinji nervously.

"The name's Misato. Misato Katsuragi."

"Nice to meet you Ms. Katsuragi."

"Skip the formalities. Call me Misato."

"Uh, ok."

* * *

"The target has been completely eliminated, sir," a technician to one of the generals.

"Well... it looks the so-called secret weapon weren't needed after all!" the general cheered. The UN had always been speculative about the Evas and whether they would work. The chance show that they didn't was great, as now the UN won't waste anymore money on them.

However, when that same technician yelled "Energy readings are being detected," the generals started fuming with rage.

"No! It's impossible! No living being can survive something like that!"

"Well, well," Fuyutsuki said, "Why am I not surprised at all?"

* * *

Driving with Misato started out calm and peaceful, but soon became a living hell. Misato ended up talking on the phone, while driving neverheless, and wouldn't stop talking after that point.

Shinji liked peace and quiet. He enjoyed it when people weren't around, not when they were berating him with question after question.

Eventually, he got to a underground bunker were a sign with the word "NERV" plastered on it. The symbol had a red left on it as well, combined with the words "God's In His Heaven, All Is Right With The World." Shinji asked what NERV was.

"Oh, NERV? NERV is an organization dedicated to fighting those things you saw up there. Your father works here, you know?"

The answer surprised Shinji. "Here? I didn't know he worked in such a place."

"Didn't he ever tell you what he does here?"

"Nope. He left when I was younger and never paid any attention to me. This is the first time he has called me in years."

"Sounds like you don't get along with your father. You sound just like me." As she was saying that however, they were entering the deepest part of the tunnel. Passing the light up ahead, it revealed a beautiful sight of a landscape with gorgeous skyscrapers that glistened in the sunlight.

"Wow! The geofront!" Shinji yelled with wonder.

"Yep. NERV uses it to protect ourselves from the Angels. It's incredibly difficult from them to get in, and even harder for the to penetrate own walls." She pointed to a giant, pyramid like structure in the centre.

"Welcome to NERV, Shinji."

* * *

"Ikari, are you sure about this?"

"Yes, I am," Gendo responded with authority, "He is the only that can be used. Rei is currently in intensive care, and the Second Child has yet to arrive. So he is the only one able to even use it."

Fuyutsuki was concerned. While he trusted Gendo's judgement, he was more concerned for the safety of whoever of the pilot was. The last test with Unit 00 went terribly wrong, leaving both the pilot AND the Eva in bad condition.

"Do you truly think your son is the Third Child?"

"Yes, I do." And with that Gendo just walked off.

"And yet you expect him to cooperate after 12 years of neglect?" Fuyutsuki muttered to himself as Gendo left.

* * *

"Come on, where is it?" Misato was once again lost. Her and Shinji had been travelling around HQ for about 90 minutes trying to find a single spot.

Then again, it wasn't her fault. The place was huge! There were dozens of quarters and apartments for the people there, despite in reality not there actually being much. Shinji pondered this. Why is this place so big? Wouldn't it be better for your HQ to be smaller?

"We've passed this spot twice already," Shinji responded.

"Well, no matter. We'll find it eventually. I'm new here as well, so yeah." Goddamnit, wondered Shinji, she doesn't even know where she's going!

"Ah look, an elevator. I'm pretty sure that's where we need to go."

"You were pretty sure about that lift about 20 minutes ago..." Both Misato and Shinji got into the elevator.

After about 3 floors, the elevator stopped and opened to reveal a young blonde woman with a lab coat. Misato obviously knew her because of the surprised look on her face.

"Hi Ritsuko..." said Misato.

"Misato, you need to start learning your way around this place," Ritsuko said with a hint of authority.

"I'm sorry. I was just bringing the Third Child."

"Ah, so this is him. Hello there. My name is Ritsuko Akagi." Shinji looked up at Ritsuko.

"Oh, hi," Shinji answered, "My name's Shinji Ikari."

"I know who you are. I was informed by Mr. Ikari himself." Shinji sighed. It seems everybody here will know who he is now.

* * *

After some techno babble from Ritsuko to Misato about something not being able to work (It's probably a computer, he thought), he entered a large, dark room. The doors were closed behind him, and then everything went completely black.

"Ah! I can't see!" Shinji yelled. After he said that, the lights turned back on. Unfortunately for him, it was only to reveal a giant, purple head staring right at him with yellow eyes. It had green stripes on it as well. A giant horn was on the top of his head.

"It's a robot!" Shinji yelled again in shock. He took out a manual that Misato had given him on the way there and started flipping through it looking for the robot.

"You won't find it in there," Ritsuko stated bluntly. Shinji looked up confused. "What you are looking at is the Evangelion known as Unit 01. It is the last hope for humanity against the Angels."

Shinji decided to ask the unavoidable question: "Is this... my father's work?"

"Correct!"

Shinji looked up to see where the voice was coming from. And up on a balcony, he saw his father, red glasses and all, standing over him.

"It's been a while."


	2. S1,E2: Berserk

**Episode 2: Berserk**

10 Years Ago

It was a rather cloudy day. The sun was blocked out, and it had rained earlier in the day. Because of that, it smelled of fresh water. Nobody was outside, and it was peaceful.

Except for the sound of a young boy's tears, screaming "Father! Father!" over and over again.

"This is for the best of both of us. Good luck son." Gendo entered the train and left Shinji on the side of the train. Alone, with no mother to care for him. He was abandoned. Nobody cared about what to him, he thought.

That thought stayed with him for the years to come.

Now

"Father..." Shinji said to himself. He had not seen his father since he was 4. He would never forget the fact that he left him with nothing. He hated him for that, no, he despised.

"Captain, it's time to move out," Gendo said to Misato. Shinji looked at Misato. She was a captain? He thought she seemed so calm and laid back, she didn't have to personality of a Captain.

"But Unit 00 isn't even working yet! Wait a minute, you're using Unit 01?!" Misato yelled, "But we don't if it works!"

"We have to try anyways!" said Ritsuko to Misato, "We have no other choice. The UN forces can't dent the damn thing and we need to protect Central Dogma!"

"I know that... but we don't have a pilot! Rei is still injured and the Second Child is still in Germany!"

"Well we just got one."

"No... no you can't be serious! He hasn't had any training at all, no sync ratio tests, no nothing!"

"Captain, I suggest you stand down! You know better then anybody that we need him to pilot!" Misato opened to say something, but stopped herself. Fighting would do her no good against Ritsuko.

"Yes ma'am," she said sadly.

"Shinji Ikari?" Ritsuko said to Shinji. Shinji looked up nervously. He had a feeling that he knew what she was going to ask. "You are the new pilot."

"What?" said Shinji, though in reality he wasn't really that surprised. Shinji looked up at his father, "Is this why you sent for me?"

"I think it has been made clear why you were sent here," Gendo replied in his usual stoic, expressionless manner.

"But why me? I'm just a kid!"

"Because you are the only one who can."

"But I can't! I've never even seen one of these things before! There's no way I can do this!" By this point, Gendo was visibly frustrated.

"If your going to do it, do it now! If not, then leave!" His voice echoed throughout the whole facility. Shinji stayed quiet for a bit. What if he did pilot it? What would happen then? No, he couldn't pilot it. He didn't even know what the damn thing was!

Suddenly, a shake came over above. In the city, the Angel had fired one of it's attacks, resulting in a cross shaped explosion.

"It's getting closer..." mumbled Gendo to himself. He looked back down at Shinji. Was he going to pilot?

"Shinji... please. We need you," Misato was begging Shinji by this point.

"But I've don't even know how to pilot the thing!" yelled Shinji, "Why did I come anyways?"

"Why did you come here?" asked Misato. Shinji looked surprised by the question. Usually he just did what people told him to do. That's why he came. "You mustn't run away, Shinji. You must confront this."

"I know that! I just... can't." Misato was out of options. She just turned her head over to Gendo and shook it. Gendo contacted Fuyutsuki over the intercom.

"Wake up Rei," Gendo ordered Fuyutsuki.

"Can you use her?" Fuyutsuko asked.

"She's not dead yet."

"...Understood sir."

Shinji could hear the Evangelion start to power down as it's eyes stopped glowing yellow. Ritsuko yelled some sciencey techno babble, and Misato left.

Shinji came to realization that he wasn't even needed here. They had another pilot! Did his father just bring him to make fun of him? He didn't really care about him at all. Neither did anyone else in this hell hole.

Just then, a group of doctors came out from the elevator with a injured girl on a dolly. The girl had blue hair, bandages everywhere, and piercing red eyes. So this is the Rei they were talking about, Shinji thought. She reminded him of his mother from some strange reason.

The doctors quickly unhooked her from the hospital equipment and left the premises. As Rei attempted to stand up, emphasis on attempted, she groaned in pain and started breathing heavily. Even breathing seemed hard for her.

Shinji stood in shock. How could this girl pilot? She was incredibly injured, and looked so fragile. She just...couldn't!

He knew what he had to do.

"I'll do it!" he yelled, "I'll pilot it!"

* * *

"Inserting entry plug!" yelled one of engineers working the Evangelion. Shinji only saw black. It was completely dark inside, with no visible light with the exception of the flashing buttons. Shinji wondered why he was doing this. Was it for a sense of entitlement? Is it pity for that girl? Or was it... for his father.

Shinji shook his head at the thought. No, he thought, I never do anything for my father. He still felt resentment towards him for leaving.

Suddenly, the lights began to turn on. And this reddish-orange liquid began to fill the tank.

"Ah!" yelled Shinji, "What is this stuff?"

"It's ok Shinji," Ritsuko said on the other end, "It's LCL, a breathable liquid. You'll get used to it." Shinji started breathing it in. It tasted like blood. Yuck.

Then, out of the blue, he could finally start to see though the cockpit. It was rather natrual too, like it was his own 2 eyes.

"Sync ratio at 41.3%," he heard Maya, one of the technicians, say over the speaker. That must be the way I control the Eva, Shinji thought.

Technicians and mechanics from all sides prepared the Eva for launch. As the Eva rose up from it's platform, Shinji could see more of NERV. It was pretty complex facility, with lifts and cranes everywhere. Shinji couldn't whether the place was still in production or it just needed these to get everywhere. Everything was so... confusing to him.

He heard the Eva grind to a halt. Lock bolts grinded into place at the bottom of the platform and the gates opened up.

"We are go for launch!" he heard Ritsuko yell on the other side. He also heard a bit of conversation between Misato and his father, but couldn't make a lot of it. Stuff about how "unless we defeat the Angels, we have no future."

"Eva Launch!" yelled Misato.

Suddenly, the Eva rose up and Shinji felt the shock go through him as he was lifted up. And then, out of nowhere, it all just came to a screeching halt. Shinji saw the Angel first hand and saw it's red core light up.

"Ok Shinji," said Ritsuko to a confused and utterly terrified Shinji, "Just concentrate on walking for now."

Shinji just thought about walking towards to the Angel. The Eva took one step forward. The ground shook as it walked and a phone booth near it cracked. Shinji decided to take another step forward. This time however, the Eva lost balance and fell flat on it's face. Shinji felt the pain from that fall. How he could feel it, he thought.

"Shinji, are you alright?" asked Misato worriedly over the com, "Hurry! You need to get up!" Shinji looked up and saw the Angel hovering above him.

The Angel grabbed the skull plate of the Eva with one hand. It's other hand grabbed onto the Eva's arm. It pulled on it, causing massive amounts of pain for Shinji. He screamed. The pain was unbearable.

"Calm down Shinji, that's not your real arm!" Shinji paid no attention to Misato.

The Angel stopped pulling and began to squeeze instead. In fact, it squeezed so hard that the Eva's arm snapped. Then, with it's purple lance in it's arm, began to stab through the Eva's head.

Shinji's grabbed his head in pain. Blood started coming out of his eye, and trickled down his face. The screen in the front began to crack. Then the spear went through the Eva's head and it flew back and the Eva hit a skyscraper. The spear retracted and the Eva's head began spout blood. Shinji fell unconscious.

* * *

"The pilot has become unresponsive!" yelled Makoto.

"Status report!' yelled Misato at the 3 technicians.

"The circuits are breaking off! No life signs detected!" Maya screamed.

"Unit 1 has gone 100% silent!" Aoba exclaimed. Misato and Ritsuko had no idea what to do. Rei couldn't pilot, and Shinji was unresponsive.

"We have no choice..." Misato said, "Abort the operation! Rescue the pilot at all costs!"

"We can't! It's not accepting the signal!"

"What did you say?" On the screen, they saw the Eva reactivate. The Eva's eyes glowed yellow and it's mouth opened. The entire headquaters were in shock. The unthinkable just happened.

"Berserker..." whispered Ritsuko.

The Eva roared and got on it's hind legs. It jumped up and launched itself forward towards the Angel. It landed to top of it and started hit it. The Angel sent it back, but the Eva landed on the ground in front of it, sending debris and concrete up into the air.

The Eva turned around and began to run towards it. The Angel had an AT Field, however, and it stopped the Eva dead in it's tracks.

"No, not now!" yelled Misato.

"It can't get near it now!" responded Ritsuko.

The Eva held out it's arm and it regenerated itself. The arm was good as new! It then grabbed hold of the Angel's AT Field and began to rip it apart.

"The Eva has activated it's own AT Field! It's neutralizing the faze space!" yelled Maya.

The Eva ripped the AT Field in two. The Angel now had nothing to defend itself. The Eva grabbed both of it's arms and broke them in half. Blood poured out of the wounds. It kicked it back where it crashed into a building.

Out of control, the Eva ran towards the Angel and launched it backwards, taking it and the building with it. The Eva, now on top of the Angel, began punch at the pulsing red core. Unable to do anything, it ripped open the Angel's chest and grabbed one of it's teeth. Ripping it off, it began to use it like a spear and tried destroy the red core. When it began to crack, the Angel screeched and wrapped itself around the Eva. It began to glow.

"It's going to self-destruct!" exclaimed Misato.

The Angel exploded, causing a giant purple cross to form where it once was. After a few seconds, the brightness died down. On the screen at NERV, they saw the Eva, partly destroyed, walking towards them.

"Is that..." whispered Ritsuko.

"...Eva's true form?" Misato replied back.

* * *

Shinji woke up to the sound of talking. People were saying on how that his life signs were returning, or how they need to get him out of the Eva soon. All he heard though was a massive crash. He looked to his right and saw the unthinkable.

There, in the reflection of a skyscraper, stood the face a creature. What creature, he could not say. Was that the Eva, he thought.

The creature's side began to slide open. A round, green object appeared, with a giant black hole in the middle. The stared at Shinji until three more black dots appeared.

And then, all the city heard, was the scream of a boy in the night.


End file.
